Wilks signed with the Orlando Magic on September 30, 2008. In the pre season game on October 26, 2008 he tore his ACL in his right knee and missed the whole regular season. He was traded to the Memphis Grizzlies on February 19, 2009. After leaving the Memphis Grizzlies, Wilks signed a contract with the Oklahoma City Thunder on November 26. He was waived by Oklahoma City on December 22, 2009, when the team acquired Eric Maynor. This was his second stint with the franchise.
Wilks wore number 29 throughout his NBA career (with the exception of his stint with the Spurs, in which he wore 11), as a tribute to Milwaukee's 29th Street playground where he grew up playing the game.
On August 25, 2010, he signed a deal with Polish league champion Asseco Prokom Gdynia but was waived in January 2011.